Generate Invoice from SO without Shipping Items - Down Payment Required

We have some customers who are on credit hold. We require that they pay either a percentage of the order or the entire order before the items are shipped. How would we create an invoice from the sales order listing the items and their cost and then once they pay ship the items?  We are a relatively small privately owned company.

It would basically be nice to have a special line item on the Sales Order that is for Down payment or Pre-payment that could be invoiced and then once received the rest of the items could ship and would generate an invoice amount of the total order less the pre-payment. 

Any help is appreciated.

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    We do this on a regular basis when requiring a down payment for a large order or because of a similar credit issue. We created a miscellaneous item code (/Downpayment) that is added to the invoice. All the sales order items are listed with a shipped quantity of zero. Then when shipped and the final invoice is generated, simply add the downpayment code again as a negative to correctly reflect the balance due.

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    We do this on a regular basis when requiring a down payment for a large order or because of a similar credit issue. We created a miscellaneous item code (/Downpayment) that is added to the invoice. All the sales order items are listed with a shipped quantity of zero. Then when shipped and the final invoice is generated, simply add the downpayment code again as a negative to correctly reflect the balance due.

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